Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Gene Rank description Network Comparison Type Value Type Interaction Map red Filtered green network_comparison

Results: HTML CSV LaTeX

Showing element 6408 to 6457 of 29840 in total

Interaction Map

: High confidence

Rank	description	Network Comparison Type	Value Type	red	Filtered	green	network_comparison
401	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]	Subtracted	Ranked	20914	0	20558	356
	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	Subtracted	Ranked	254.434	1	236.224	18.21
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Divided	Measured	548.5	0	527.5	1.03981
	phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205]	Subtracted	Squared	28188.7	1	33982.7	5794
	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]	Divided	Ranked	207.908		226.218	1.08807
	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]	Divided	Rooted	116.707		106.044	1.10055
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	Subtracted	Squared	12.5892	0	5.42219	7.16701
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Divided	Ranked	12305.9	0	11904.9	1.03368
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Subtracted	Rooted	55.9231	1	62.0565	6.1334
402	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	Divided	Rooted	21.6987	0	22.4088	1.03273
	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	Divided	Ranked	10562.4		10918	1.03367
		Subtracted	Ranked	10562.4		10918	355.6
	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	Subtracted	Measured	6230.94	1	7168.2	937.26
	brain protein 16. [refseq;acc:nm_016458]	Divided	Squared	2538.95	0	2371.77	1.07049
	cab2. [refseq;acc:nm_033419]	Subtracted		0	0	7.16592	7.16592
	endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]	Divided		39472	1	48393.1	1.22601
	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537]	Divided	Rooted	50.1918		55.2294	1.10037
	gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104]	Subtracted	Squared	28190.4		33984.1	5793.7
	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	Subtracted	Ranked	231.802		249.983	18.181
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Divided	Measured	5201.41		4479.76	1.16109
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Subtracted		12.6208	0	39.8063	27.1855
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Divided		548.5	0	527.5	1.03981
	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	Subtracted	Rooted	59.5128	1	65.604	6.0912
	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]	Divided	Ranked	207.908	1	226.218	1.08807
	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	Subtracted	Rooted	17.8274	0	17.1002	0.7272
403	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]		Squared	28190.4	1	33984.1	5793.7
	calcyphosine. [swissprot;acc:q13938]		Rooted	59.5128		65.604	6.0912
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Divided	Measured	5201.41		4479.76	1.16109
	glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]	Divided	Squared	39463.9		48362.1	1.22548
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Subtracted	Rooted	15.4896	0	14.7645	0.7251
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	Divided	Squared	1872.12		1754.91	1.06679
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Subtracted	Measured	2290.09		2264.37	25.72
	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	Subtracted	Ranked	228.468	1	246.338	17.87
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Divided	Measured	548.5	0	527.5	1.03981
	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]		Rooted	59.6834	1	65.6741	1.10037
	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]		Ranked	207.908	1	226.218	1.08807
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]		Rooted	19.4322	0	20.0671	1.03267
	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Subtracted	Measured	6259.3	1	7190.91	931.61
	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]		Squared	94.678	0	87.5656	7.1124
	scribble. [refseq;acc:nm_015356]		Ranked	12370.5		12719	348.5
	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	Divided	Ranked	9783.63		10111.2	1.03348
404	40s ribosomal protein s3a. [swissprot;acc:p49241]		Rooted	34.0198		32.9781	1.03159
	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]		Squared	26819.1	1	32855.4	1.22507
	alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733]	Subtracted	Squared	28190.4		33984.1	5793.7
	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001]		Ranked	228.463		246.33	17.867
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]		Rooted	59.5128		65.604	6.0912
	dna repair protein rad52 homolog. [swissprot;acc:p43351]	Divided	Ranked	207.908		226.218	1.08807
	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	Subtracted	Squared	3228.32	0	3221.55	6.77
	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060]	Subtracted	Measured	7802.31	1	8731.82	929.51
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Divided	Measured	5201.41	1	4479.76	1.16109

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.

- http://analysis.yellowcouch.org/